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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: Jun 22, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Reference map for liquid chromatography-mass spectrometry-based quantitative proteomics.

Yeoun Jin Kim1, Brian Feild, William Fitzhugh

  • 1Celera, Rockville, MD 20850, USA.

Analytical Biochemistry
|June 23, 2009
PubMed
Summary
This summary is machine-generated.

A new reference map method enhances proteomic analysis in liquid chromatography-mass spectrometry (LC-MS). This approach improves peptide identification confidence and throughput, even for low-intensity or complex samples, simplifying high-throughput proteomics.

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An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry

Published on: April 17, 2018

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Accurate mass and time (AMT) tag strategy is crucial for high-throughput liquid chromatography-mass spectrometry (LC-MS) proteomics.
  • The complexity of the human proteome necessitates highly accurate mass measurements for confident peptide identification.

Purpose of the Study:

  • To develop a novel method for building a reference map to improve peptide identification confidence in LC-MS proteomics.
  • To enable relaxed mass error criteria while maintaining high confidence in peptide identifications.

Main Methods:

  • Cysteine-containing peptides were collected from T47D cells and fractionated using strong cationic exchange chromatography (SCX).
  • LC-tandem mass spectrometry (MS/MS) data from SCX fractions were combined to create a comprehensive reference map.
  • The reference map was utilized to guide peptide identification in subsequent proteomic analyses, bypassing the SCX step.

Main Results:

  • The developed reference map allows for relaxed mass error criteria, yet delivers high confidence in peptide identifications.
  • Skipping the SCX fractionation step after building the reference map was feasible for further analyses.
  • Reference-driven identification significantly increased proteomic coverage and throughput, identifying low-intensity or complex peptides.
  • The reference map facilitated quantitation by enabling targeted peptide intensity extraction and incorporating theoretical isotope distribution models.

Conclusions:

  • The reference map strategy offers a powerful tool for enhancing high-throughput LC-MS proteomics.
  • This method improves proteomic coverage and efficiency by simplifying complex sample analysis.
  • The approach aids in accurate peptide quantitation, contributing to more robust proteomic studies.